combineInteractionChangedFeats

Combine ICF scores in a pairwise manner.

combineInteractionChangedFeats(
  icfObject,
  selected_ints = NULL,
  selected_feats = NULL,
  specific_feats_1 = NULL,
  specific_feats_2 = NULL,
  min_cells = 5,
  min_int_cells = 3,
  min_fdr = 0.05,
  min_spat_diff = 0,
  min_log2_fc = 0.5,
  do_parallel = TRUE,
  verbose = TRUE
)

combineICF(
  icfObject,
  selected_ints = NULL,
  selected_feats = NULL,
  specific_feats_1 = NULL,
  specific_feats_2 = NULL,
  min_cells = 5,
  min_int_cells = 3,
  min_fdr = 0.05,
  min_spat_diff = 0,
  min_log2_fc = 0.5,
  do_parallel = TRUE,
  verbose = TRUE
)

Arguments

icfObject

ICF (interaction changed feat) score object

selected_ints

subset of selected cell-cell interactions (optional)

selected_feats

subset of selected Features (optional)

specific_feats_1

specific Featureset combo (need to position match specific_feats_2)

specific_feats_2

specific Featureset combo (need to position match specific_feats_1)

min_cells

minimum number of target cell type

min_int_cells

minimum number of interacting cell type

min_fdr

minimum adjusted p-value

min_spat_diff

minimum absolute spatial expression difference

min_log2_fc

minimum absolute log2 fold-change

do_parallel

run calculations in parallel with mclapply

verbose

verbose

Value

`combIcfObject` that contains the filtered differential feature scores

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> 
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"
g_icf <- findInteractionChangedFeats(g,
    cluster_column = "leiden_clus",
    selected_feats = c("Gna12", "Ccnd2", "Btbd17"),
    nr_permutations = 10
)
#> Error in loadNamespace(x): there is no package called ‘future.apply’

cicf <- combineInteractionChangedFeats(g_icf)
#> Error in eval(expr, envir, enclos): object 'g_icf' not found
force(cicf)
#> Error in eval(expr, envir, enclos): object 'cicf' not found
combineICF(g_icf) # this is a shortened alias
#> Error in eval(expr, envir, enclos): object 'g_icf' not found